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Modernise messaging infrastructure with cli support

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Rewrites message_(), warning_(), stop_() to use cli::cli_inform(),
cli::cli_warn(), and cli::cli_abort() when the cli package is available,
with a fully functional plain-text fallback for environments without cli.

Key changes:
- New cli_to_plain() helper converts cli inline markup ({.fun}, {.arg},
  {.val}, {.field}, {.cls}, {.pkg}, {.href}, {.url}, etc.) to readable
  plain-text equivalents for the non-cli fallback path
- word_wrap() simplified: drops add_fn, ANSI re-index algorithm, RStudio
  link injection, and operator spacing hack; returns pasted input unchanged
  when cli is available
- stop_() no longer references AMR_env$cli_abort; uses pkg_is_available()
  directly; passes sys.call() objects to cli::cli_abort() call= argument
- Removed add_fn parameter from message_(), warning_(), and word_wrap()
- All call sites across R/ updated: add_fn arguments removed, some paste0-
  based string construction converted to cli glue syntax ({.fun as.mo},
  {.arg col_mo}, {n} results, etc.)
- cli already listed in Suggests; no DESCRIPTION dependency changes needed

https://claude.ai/code/session_01XHWLohiSTdZvCutwD7ag2b
This commit is contained in:
Claude
2026-03-18 12:10:17 +00:00
parent 8439e9c1d2
commit ad31fba556
16 changed files with 252 additions and 279 deletions
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41
R/interpretive_rules.R
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@@ -192,19 +192,19 @@ interpretive_rules <- function(x,
stop_if(
!is.na(ampc_cephalosporin_resistance) && !any(c("expert", "all") %in% rules),
"For the `ampc_cephalosporin_resistance` argument to work, the `rules` argument must contain `\"expert\"` or `\"all\"`."
"For the {.arg ampc_cephalosporin_resistance} argument to work, the {.arg rules} argument must contain {.code \"expert\"} or {.code \"all\"}."
)
add_MO_lookup_to_AMR_env()
if ("custom" %in% rules && is.null(custom_rules)) {
warning_("in `eucast_rules()`: no custom rules were set with the `custom_rules` argument",
warning_("in {.fun eucast_rules}: no custom rules were set with the {.arg custom_rules} argument",
immediate = TRUE
)
rules <- rules[rules != "custom"]
if (length(rules) == 0) {
if (isTRUE(info)) {
message_("No other rules were set, returning original data", add_fn = font_red, as_note = FALSE)
message_("No other rules were set, returning original data", as_note = FALSE)
}
return(x)
}
@@ -232,7 +232,7 @@ interpretive_rules <- function(x,
q_continue <- utils::menu(choices = c("OK", "Cancel"), graphics = FALSE, title = txt)
}
if (q_continue %in% c(FALSE, 2)) {
message_("Cancelled, returning original data", add_fn = font_red, as_note = FALSE)
message_("Cancelled, returning original data", as_note = FALSE)
return(x)
}
}
@@ -241,7 +241,7 @@ interpretive_rules <- function(x,
# -- mo
if (is.null(col_mo)) {
col_mo <- search_type_in_df(x = x, type = "mo", info = info)
stop_if(is.null(col_mo), "`col_mo` must be set")
stop_if(is.null(col_mo), "{.arg col_mo} must be set")
}
decimal.mark <- getOption("OutDec")
@@ -459,7 +459,7 @@ interpretive_rules <- function(x,
x$gramstain <- mo_gramstain(x[, col_mo, drop = TRUE], language = NULL, info = FALSE)
x$genus_species <- trimws(paste(x$genus, x$species))
if (isTRUE(info) && NROW(x.bak) > 10000) {
message_("OK.", add_fn = list(font_green, font_bold), as_note = FALSE)
message_("OK.", as_note = FALSE)
}
n_added <- 0
@@ -595,23 +595,13 @@ interpretive_rules <- function(x,
} else {
if (isTRUE(info)) {
cat("\n")
message_(paste0(
font_red("Skipping inhibitor-inheritance rules defined by this AMR package: setting "),
font_green_bg(" S "),
font_red(" to drug+inhibitor where drug is "),
font_green_bg(" S "),
font_red(", and setting "),
font_rose_bg(" R "),
font_red(" to drug where drug+inhibitor is "),
font_rose_bg(" R "),
font_red(". Add \"other\" or \"all\" to the `rules` argument to apply those rules.")
))
message_("Skipping inhibitor-inheritance rules defined by this AMR package: setting S to drug+inhibitor where drug is S, and setting R to drug where drug+inhibitor is R. Add \"other\" or \"all\" to the {.arg rules} argument to apply those rules.")
}
}
if (!any(c("all", "custom") %in% rules) && !is.null(custom_rules)) {
if (isTRUE(info)) {
message_("Skipping custom EUCAST rules, since the `rules` argument does not contain \"custom\".")
message_("Skipping custom EUCAST rules, since the {.arg rules} argument does not contain {.code \"custom\"}.")
}
custom_rules <- NULL
}
@@ -673,8 +663,7 @@ interpretive_rules <- function(x,
if (isTRUE(info)) {
message_("Using column '", cols_ab[names(cols_ab) == ab],
"' as ", ab_name(ab_s, language = NULL, tolower = TRUE),
" since a column '", ab_s, "' is missing but required for the chosen rules",
add_fn = font_red
" since a column '", ab_s, "' is missing but required for the chosen rules"
)
}
cols_ab <- c(cols_ab, stats::setNames(unname(cols_ab[names(cols_ab) == ab]), ab_s))
@@ -898,7 +887,7 @@ interpretive_rules <- function(x,
for (i in seq_len(length(custom_rules))) {
rule <- custom_rules[[i]]
rows <- tryCatch(which(eval(parse(text = rule$query), envir = x)),
error = function(e) stop_(paste0(conditionMessage(e), font_red(" (check available data and compare with the custom rules set)")), call = FALSE)
error = function(e) stop_(conditionMessage(e), " (check available data and compare with the custom rules set)", call = FALSE)
)
cols <- as.character(rule$result_group)
cols <- c(
@@ -1073,7 +1062,7 @@ interpretive_rules <- function(x,
warn_lacking_sir_class <- warn_lacking_sir_class[order(colnames(x.bak))]
warn_lacking_sir_class <- warn_lacking_sir_class[!is.na(warn_lacking_sir_class)]
warning_(
"in `eucast_rules()`: not all columns with antimicrobial results are of class 'sir'. Transform them on beforehand, with e.g.:\n",
"in {.fun eucast_rules}: not all columns with antimicrobial results are of class 'sir'. Transform them on beforehand, with e.g.:\n",
" - ", x_deparsed, " %>% as.sir(", ifelse(length(warn_lacking_sir_class) == 1,
warn_lacking_sir_class,
paste0(warn_lacking_sir_class[1], ":", warn_lacking_sir_class[length(warn_lacking_sir_class)])
@@ -1108,7 +1097,7 @@ eucast_rules <- function(x,
rules = getOption("AMR_interpretive_rules", default = c("breakpoints", "expected_phenotypes")),
...) {
if (!is.null(getOption("AMR_eucastrules", default = NULL))) {
warning_("The global option `AMR_eucastrules` that you have set is now invalid was ignored - set `AMR_interpretive_rules` instead. See `?AMR-options`.")
warning_("The global option {.code AMR_eucastrules} that you have set is now invalid was ignored - set {.code AMR_interpretive_rules} instead. See {.code ?AMR-options}.")
}
interpretive_rules(x = x, col_mo = col_mo, info = info, rules = rules, guideline = "EUCAST", ...)
}
@@ -1165,7 +1154,7 @@ edit_sir <- function(x,
isSIR <- !isNA & (new_edits[rows, cols] == "S" | new_edits[rows, cols] == "I" | new_edits[rows, cols] == "R" | new_edits[rows, cols] == "SDD" | new_edits[rows, cols] == "NI" | new_edits[rows, cols] == "WT" | new_edits[rows, cols] == "NWT" | new_edits[rows, cols] == "NS")
non_SIR <- !isSIR
if (isFALSE(overwrite) && any(isSIR) && message_not_thrown_before("edit_sir.warning_overwrite")) {
warning_("Some values had SIR values and were not overwritten, since `overwrite = FALSE`.")
warning_("Some values had SIR values and were not overwritten, since {.code overwrite = FALSE}.")
}
tryCatch(
# insert into original table
@@ -1189,7 +1178,7 @@ edit_sir <- function(x,
suppressWarnings(new_edits[rows, cols][non_SIR] <<- to)
}
warning_(
"in `eucast_rules()`: value \"", to, "\" added to the factor levels of column",
"in {.fun eucast_rules}: value \"", to, "\" added to the factor levels of column",
ifelse(length(cols) == 1, "", "s"),
" ", vector_and(cols, quotes = "`", sort = FALSE),
" because this value was not an existing factor level."
@@ -1197,7 +1186,7 @@ edit_sir <- function(x,
txt_warning()
warned <- FALSE
} else {
warning_("in `eucast_rules()`: ", w$message)
warning_("in {.fun eucast_rules}: ", w$message)
txt_warning()
}
},